The beginning of the 21stCentury is marked by a realization of the increasing threat of infectious diseases worldwide and the formidable challenges posed by microbial antibiotic resistance, microbial antigenic variation, genetic latency, and emerging infectious agents. Microorganisms have evolved a confounding array of persistence mechanisms to avoid host defenses leading to established infections that result in disease or death. To address these complex problems it is essential to define at the molecular level the mechanisms underlying microbial evolution, persistence, and pathogenesis, studies that require interdisciplinary and collaborative research efforts. Thus, we describe here a university-wide interdisciplinary training program in Molecular Microbial Persistence and Pathogenesis (MMPP) for predoctoral and postdoctoral trainees that combines outstanding training resources and opportunities provided by a highly interactive team of 30 faculty mentors in the University of Pittsburgh School of Medicine, Graduate School of Public Health, and Faculty of Arts and Sciences. The rationale for the MMPP Training Program is that the immersion of predoctoral and postdoctoral trainees into an interdisciplinary program of molecular mechanistic studies of diverse viruses, bacteria, and protozoa will provide the most effective foundation to gain comprehensive expertise and experience for future critical studies of microbial persistence and pathogenesis. The MMPP training Program is designed to attract the best and the brightest trainees, create unique opportunities and environment for didactic and research training relevant to microbial persistence and pathogenesis, to enhance research collaborations among different university units, and to optimize the utilization of research and training resources. Thus, the goal of the MMPP Training Program is to produce the next generation of independent investigators with unique perspective of interdisciplinary and collaborative research training required to elucidate at the molecular level the mechanisms of microbial persistence and pathogenesis and to use this information to develop new and effective prevention and treatment strategies for infectious diseases.